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I'm going to guess what happens here is that the file is being updated but then is being updated again by the other tab. (You can probably confirm this by looking at the file's modification times. A full reproduction would make it possible for us to confirm this.)

That said, this seems surprising that it would decide to downgrade. Maybe the runner tab isn't rereading the versions file even though it decided to re-run?

It would be great to have a full reproduction here, so this is easy to test, especially since @dgreensp is working on some changes to the version solver (which may or may not be at fault here).

As a workaround, meteor update meteorhacks:kadira@2.17.3 should work (since that also writes the minimum compatible version to .meteor/packages). If that doesn't work there's a pretty serious issue.